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Updated: Jul 9, 2025
Visualization, Quantification, and Mapping of Immune Cell Populations in the Tumor Microenvironment
Published on: March 25, 2020
Highly Multiplexed 3D Profiling of Cell States and Immune Niches in Human Tumours
Clarence Yapp1,2, Ajit J Nirmal1,2,3, Felix Zhou4
1Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
Insights
This study introduces a high-resolution 3D imaging technique for detailed tissue analysis. The method reveals new insights into cell interactions and states during early melanoma development and immunoediting.
Area of Science:
- Cellular Biology
- Cancer Research
- Imaging Technology
Background:
- Tissue homeostasis relies on cellular composition, organization, and interactions.
- Current spatial omics lack resolution for subtle cellular features.
- High-resolution imaging is needed to understand complex tissue microenvironments.
Purpose of the Study:
- To develop and validate a high-resolution 3D imaging approach for detailed tissue analysis.
- To characterize cellular interactions and states in melanoma.
- To gain insights into early tumor formation and immunoediting.
Main Methods:
- Combined cyclic immunofluorescence (CyCIF) with confocal microscopy on thick tissue sections (30-40 microns).
- Enabled sub-micron scale organelle and structure characterization alongside millimeter-scale spatial features.
- Improved cell phenotyping accuracy and cell proximity scoring using plasma membrane apposition.
Main Results:
- Precise phenotyping of pre-invasive melanoma revealed plastic melanocytic cells and localized interferon signaling niches.
- Identified diverse juxtacrine, membrane-membrane, and neighborhood interactions between T cells in melanoma.
- Demonstrated functional states through morphological analysis of cell interactions.
Conclusions:
- The 3D imaging approach provides unprecedented detail of tissue microenvironments.
- Revealed novel insights into cellular plasticity and interactions during early melanoma progression.
- Highlights the potential for detailed tissue phenotyping previously limited to cultured cells.
Abstract:
Diseases like cancer involve alterations in in cell proportions, states, and local interactions as well as complex changes in 3D tissue architecture. However, disease diagnosis and most multiplexed spatial profiling studies rely on inspecting thin (4-5 micron) tissue specimens. Here, we use confocal microscopy and cyclic immunofluorescence (3D CyCIF) to show that few if any cells are intact in these thin sections; this reduces the accuracy of cell phenotyping and interaction analysis. In contrast, high-plex 3D CyCIF imaging of intact cells in thick tissue sections enables accurate quantification of marker proteins and detailed analysis of intracellular structures and organelles. Precise imaging of cell membranes also makes it possible to detect juxtacrine signalling among interacting tumour and immune cells and reveals the formation of spatially-restricted cytokine niches. Thus, 3D CyCIF provides insights into cell states and morphologies in preserved human tissues at a level of detail previously limited to cultured cells.
